Análises de WGCNA foram conduzidas utilizando amostras temporais de RNA-Seq de Agave sisalana, alinhadas ao genoma CDS (incluindo isoformas) por meio do Kallisto. Os valores de TPM de todos os genes e suas respectivas isoformas foram agregados. Em seguida, a matriz foi normalizada utilizando o método TMM. Por fim, aplicou-se um filtro para remover genes com valores inferiores a 5 em todas as amostras, reduzindo o número de genes de 42.200 para 21.362 genes.
Article
RNAseq
Genome
Abaixo estão os IDs completos e abreviados de cada amostra, com o objetivo de facilitar a visualização dos resultados. Em alguns gráficos, os IDs podem não incluir o número da replicata, indicando que o resultado representa a média das replicatas.
Irrigated
Agavesisalana_Irrigated_Sample01.12h_Replicate1_L001 = As_I_S01.12h_R1_L001
Agavesisalana_Irrigated_Sample01.12h_Replicate1_L003 = As_I_S01.12h_R1_L003
Agavesisalana_Irrigated_Sample01.12h_Replicate2_L001 = As_I_S01.12h_R2_L001
Agavesisalana_Irrigated_Sample01.12h_Replicate2_L003 = As_I_S01.12h_R2_L003
Agavesisalana_Irrigated_Sample01.12h_Replicate3_L001 = As_I_S01.12h_R3_L001
Agavesisalana_Irrigated_Sample01.12h_Replicate3_L003 = As_I_S01.12h_R3_L003
Agavesisalana_Irrigated_Sample01.12h_Replicate4_L008 = As_I_S01.12h_R4_L008
Agavesisalana_Irrigated_Sample01.12h_Replicate5_L008 = As_I_S01.12h_R5_L008
Agavesisalana_Irrigated_Sample02.18h_Replicate1_L001 = As_I_S02.18h_R1_L001
Agavesisalana_Irrigated_Sample02.18h_Replicate1_L003 = As_I_S02.18h_R1_L003
Agavesisalana_Irrigated_Sample02.18h_Replicate2_L001 = As_I_S02.18h_R2_L001
Agavesisalana_Irrigated_Sample02.18h_Replicate2_L003 = As_I_S02.18h_R2_L003
Agavesisalana_Irrigated_Sample02.18h_Replicate3_L001 = As_I_S02.18h_R3_L001
Agavesisalana_Irrigated_Sample02.18h_Replicate3_L003 = As_I_S02.18h_R3_L003
Agavesisalana_Irrigated_Sample02.18h_Replicate4_L001 = As_I_S02.18h_R4_L001
Agavesisalana_Irrigated_Sample02.18h_Replicate4_L003 = As_I_S02.18h_R4_L003
Agavesisalana_Irrigated_Sample02.18h_Replicate5_L001 = As_I_S02.18h_R5_L001
Agavesisalana_Irrigated_Sample02.18h_Replicate5_L003 = As_I_S02.18h_R5_L003
Agavesisalana_Irrigated_Sample03.24h_Replicate1_L001 = As_I_S03.24h_R1_L001
Agavesisalana_Irrigated_Sample03.24h_Replicate1_L003 = As_I_S03.24h_R1_L003
Agavesisalana_Irrigated_Sample03.24h_Replicate2_L001 = As_I_S03.24h_R2_L001
Agavesisalana_Irrigated_Sample03.24h_Replicate2_L003 = As_I_S03.24h_R2_L003
Agavesisalana_Irrigated_Sample03.24h_Replicate3_L001 = As_I_S03.24h_R3_L001
Agavesisalana_Irrigated_Sample03.24h_Replicate3_L003 = As_I_S03.24h_R3_L003
Agavesisalana_Irrigated_Sample03.24h_Replicate4_L001 = As_I_S03.24h_R4_L001
Agavesisalana_Irrigated_Sample03.24h_Replicate4_L003 = As_I_S03.24h_R4_L003
Agavesisalana_Irrigated_Sample03.24h_Replicate5_L001 = As_I_S03.24h_R5_L001
Agavesisalana_Irrigated_Sample03.24h_Replicate5_L003 = As_I_S03.24h_R5_L003
Agavesisalana_Irrigated_Sample04.6h_Replicate1_L001 = As_I_S04.6h_R1_L001
Agavesisalana_Irrigated_Sample04.6h_Replicate1_L003 = As_I_S04.6h_R1_L003
Agavesisalana_Irrigated_Sample04.6h_Replicate2_L001 = As_I_S04.6h_R2_L001
Agavesisalana_Irrigated_Sample04.6h_Replicate2_L003 = As_I_S04.6h_R2_L003
Agavesisalana_Irrigated_Sample04.6h_Replicate3_L001 = As_I_S04.6h_R3_L001
Agavesisalana_Irrigated_Sample04.6h_Replicate3_L003 = As_I_S04.6h_R3_L003
Agavesisalana_Irrigated_Sample04.6h_Replicate4_L001 = As_I_S04.6h_R4_L001
Agavesisalana_Irrigated_Sample04.6h_Replicate4_L003 = As_I_S04.6h_R4_L003
Agavesisalana_Irrigated_Sample04.6h_Replicate5_L001 = As_I_S04.6h_R5_L001
Agavesisalana_Irrigated_Sample04.6h_Replicate5_L003 = As_I_S04.6h_R5_L003
Drought
Agavesisalana_Drougth_Sample01.12h_Replicate1_L001 = As_D_S01.12h_R1_L001
Agavesisalana_Drougth_Sample01.12h_Replicate1_L003 = As_D_S01.12h_R1_L003
Agavesisalana_Drougth_Sample01.12h_Replicate2_L001 = As_D_S01.12h_R2_L001
Agavesisalana_Drougth_Sample01.12h_Replicate2_L003 = As_D_S01.12h_R2_L003
Agavesisalana_Drougth_Sample01.12h_Replicate3_L001 = As_D_S01.12h_R3_L001
Agavesisalana_Drougth_Sample01.12h_Replicate3_L003 = As_D_S01.12h_R3_L003
Agavesisalana_Drougth_Sample01.12h_Replicate4_L001 = As_D_S01.12h_R4_L001
Agavesisalana_Drougth_Sample01.12h_Replicate4_L003 = As_D_S01.12h_R4_L003
Agavesisalana_Drougth_Sample01.12h_Replicate5_L001 = As_D_S01.12h_R5_L001
Agavesisalana_Drougth_Sample01.12h_Replicate5_L003 = As_D_S01.12h_R5_L003
Agavesisalana_Drougth_Sample02.18h_Replicate1_L001 = As_D_S02.18h_R1_L001
Agavesisalana_Drougth_Sample02.18h_Replicate1_L003 = As_D_S02.18h_R1_L003
Agavesisalana_Drougth_Sample02.18h_Replicate2_L001 = As_D_S02.18h_R2_L001
Agavesisalana_Drougth_Sample02.18h_Replicate2_L003 = As_D_S02.18h_R2_L003
Agavesisalana_Drougth_Sample02.18h_Replicate3_L001 = As_D_S02.18h_R3_L001
Agavesisalana_Drougth_Sample02.18h_Replicate3_L003 = As_D_S02.18h_R3_L003
Agavesisalana_Drougth_Sample02.18h_Replicate4_L001 = As_D_S02.18h_R4_L001
Agavesisalana_Drougth_Sample02.18h_Replicate4_L003 = As_D_S02.18h_R4_L003
Agavesisalana_Drougth_Sample02.18h_Replicate5_L001 = As_D_S02.18h_R5_L001
Agavesisalana_Drougth_Sample02.18h_Replicate5_L003 = As_D_S02.18h_R5_L003
Agavesisalana_Drougth_Sample03.24h_Replicate1_L001 = As_D_S03.24h_R1_L001
Agavesisalana_Drougth_Sample03.24h_Replicate1_L003 = As_D_S03.24h_R1_L003
Agavesisalana_Drougth_Sample03.24h_Replicate2_L001 = As_D_S03.24h_R2_L001
Agavesisalana_Drougth_Sample03.24h_Replicate2_L003 = As_D_S03.24h_R2_L003
Agavesisalana_Drougth_Sample03.24h_Replicate3_L001 = As_D_S03.24h_R3_L001
Agavesisalana_Drougth_Sample03.24h_Replicate3_L003 = As_D_S03.24h_R3_L003
Agavesisalana_Drougth_Sample03.24h_Replicate4_L001 = As_D_S03.24h_R4_L001
Agavesisalana_Drougth_Sample03.24h_Replicate4_L003 = As_D_S03.24h_R4_L003
Agavesisalana_Drougth_Sample03.24h_Replicate5_L001 = As_D_S03.24h_R5_L001
Agavesisalana_Drougth_Sample03.24h_Replicate5_L003 = As_D_S03.24h_R5_L003
Agavesisalana_Drougth_Sample04.6h_Replicate1_L001 = As_D_S04.6h_R1_L001
Agavesisalana_Drougth_Sample04.6h_Replicate1_L003 = As_D_S04.6h_R1_L003
Agavesisalana_Drougth_Sample04.6h_Replicate2_L001 = As_D_S04.6h_R2_L001
Agavesisalana_Drougth_Sample04.6h_Replicate2_L003 = As_D_S04.6h_R2_L003
Agavesisalana_Drougth_Sample04.6h_Replicate3_L001 = As_D_S04.6h_R3_L001
Agavesisalana_Drougth_Sample04.6h_Replicate3_L003 = As_D_S04.6h_R3_L003
Agavesisalana_Drougth_Sample04.6h_Replicate4_L001 = As_D_S04.6h_R4_L001
Agavesisalana_Drougth_Sample04.6h_Replicate4_L003 = As_D_S04.6h_R4_L003
Agavesisalana_Drougth_Sample04.6h_Replicate5_L001 = As_D_S04.6h_R5_L001
Agavesisalana_Drougth_Sample04.6h_Replicate5_L003 = As_D_S04.6h_R5_L003
Nenhum outlier detectado.
O valor de Soft Threshold Power utilizado nesta análise foi de: 16
## Total de genes: 21361
## Genes agrupados em módulos: 16353
## Genes não agrupados: 5008
O heatmap abaixo foi gerado a partir do heatmap anterior, que passou por um tratamento especÃfico de filtragem no script. Nesse processo, foram filtradas as interações com correlações (Corr) altamente positivas ou negativas, bem como valores de significância ideais (p-value). Os critérios de corte utilizados foram os seguintes:
Os módulos que não atenderam a esses critérios foram removidos, garantindo que apenas as interações mais relevantes fossem exibidas no heatmap.